Missing
by CharizardFreak
Summary: A terrible plague ushers in an extinction event unlike any that's ever come before. The world and the people in it are falling apart as Pokemon disappear from the planet, taking hope and sanity with them. With a vague gift and a warning from Arceus, Ash and his friends are tasked with coming up with a way to save the world. Story begins sometime during XY. Some pairings included.
1. Prologue

**Prologue: Introductions**

Serena woke with a start. The early morning sun was peeking through the cave she slept in, casting a gentle glow over her body and throwing shadows on the walls and floor. She could hear the nearby stream gurgling against the rocks. She waited for her racing heart to slow; last night's dream had frightened her for sure, but she couldn't remember a thing about it.

She stood and stretched, spreading her front legs and arching her neck, shaking her head while being careful that her antlers didn't knock at the cave walls. As she slowly awoke and became more active, her blue antlers began to shimmer and change colors. The light struck them and cast rainbow reflections on the rocks. She blinked and yawned, dipping her head down to rub her face against her foreleg. She'd been in her Pokemon form for a long time now, almost a week. She stepped out of the cave, feet clicking on the stone and eyes blinking in the sunlight, and took in her surroundings. She was in a small valley, surrounded by rocks that stretched well over her head. There was a long field of lush green grass dotted with wildflowers that stopped at a grove of trees. A stream ran from the mountains into a nearby pond. Serena approached the pond and took a long drink from the cool, clear water. When she had first arrived at this place, it had been nothing but a rocky pit with a muddy water-hole and some dead trees. Now, thanks to her presence, it was bursting with beauty and life.

But only plant life.

Serena lifted her head and scanned her little valley. She flicked her blue ears forward and listened. Aside from the faint sounds of the stream and some rustling leaves and grass, the place was silent. It had been many years now, but the silence still gave her chills. There were no chirping Fletchling, no buzzing Beedrill, no splashing Buizel. At one point in her life, you couldn't go anywhere without seeing a Pokemon. Her heart ached. She missed the Pokemon. She missed _her_ Pokemon. She missed her mom and her friends. Hell, she even missed Team Rocket… but they were all gone.

Well, not _all_ gone. Some friends remained.

Though for how long, one had to wonder. The world was falling apart without the Pokemon, and soon everything would be gone.

Serena sighed. Bending her knees, she lowered herself to the ground and laid her head in the grass. She closed her eyes and waited to fall asleep; the colored pieces on her antlers folded in and all gold turned to light blue as her body began reverting to her Neutral form. This was all she ever did these days. Sleeping passed the time, made her forget the world around her. And in some small part of her mind she hoped to one day wake up and find it had all been one long, terrible nightmare. She laughed at herself.

 _Look at you. A Xerneas, the great giver of life, curled up alone in a meadow, wishing for miracles that won't come. Pathetic, as Paul would say…_

The others were probably worried about her, but she found it was too much effort to care. Her head hurt and all she wanted to do was sleep…

...

Serena woke to the sound of sobbing. She lifted her head and looked around, but saw nothing. She thought maybe she'd imagined it, and considered \ going back to sleep, until she heard it again through the trees.

 _What in the world?_ She wondered, climbing to her feet. _No one else should be here._

She stepped cautiously through the trees, moving in that silent, graceful way Xerneas was famous for, following the cries.

 _That almost sounds like… a child?_

Serena approached one of the many cliffs that surrounded the valley. She saw a form huddled on the ground, but she kept her distance, hiding in the trees. Her eyes widened as she realized what she was seeing: A little girl was lying in the dirt at the base of a cliff, sobbing, as if in pain. Serena looked more closely and realized the girl's leg was bent, but not where it should be. Ouch.

 _Poor thing._ Serena thought as she stepped out of the trees.

The little girl heard her coming and lifted her head, only to freeze when she saw Serena. There was a look of astonishment and disbelief on her face. At first Serena was confused, but then she realized what this must look like. A Pokemon emerging from the forest to save her, and not just any Pokemon, but Xerneas, a Legendary. All the Pokemon were gone, after all. This girl was so young, had she even been around long enough to meet a Pokemon?

 _Sorry, kid,_ Serena thought to herself, with a sharp and bitter pang of sadness in her heart, _I'm not even a real one…_

The girl continued to stare as Serena came closer.

Serena hesitated, then, projecting her thoughts, asked the first thing that came to mind.

 _Are you alright?_

The girl flinched at Serena's voice, but tearfully shook her head. Serena mentally kicked herself.

 _Of course not, let's fix that leg, shall we?_

Serena focused her energy. She knew this was going to hurt, but not nearly as much as it was currently hurting this girl. Serena's antlers began to glow, all the colors of the rainbow glittering against the cliff face. A blue light shown from Serena and enveloped the small girl before her. The light turned green where the girl was injured, then after a brief pause turned red. The red light traveled back to Serena, enveloping her this time, and Serena felt a sharp, intense pain in her left hind leg. It was as if someone had snapped it in half. She gasped, startling the girl; but after a moment, the light went out, and Serena felt the pain ebb away. She looked at the girl, who was open-mouthed in astonishment.

 _You're still injured, so don't walk on it just yet. It should be less serious and not as painful now. How do you feel?_

The girl flinched again, only to realize that her leg wasn't cracked in half any more. She carefully got to her feet, and stared at her almost completely healed leg as she cautiously put weight on it. She looked back at Serena, eyes wide.

"Thank you," she said, carefully sitting back down, "Umm… I… What are you?"

Serena laughed. It felt strange, she hadn't laughed in a long time.

 _I'm… I'm Xerneas._ She replied.

The girl's eyes widened. "I thought so. I had a story book with a picture of you in it… Where have you been all this time? Are there more Pokemon out there? Why are you here by yourself? How did you survive the sickness? Why haven't you let anyone know you're still alive?"

Serena hesitated, not sure where to start. She was troubled by the girl's questions, and didn't really want to, well, _pretend_ to be Xerneas… It felt strangely sacrilegious, like she was mocking the real one.

 _I'm not really Xerneas… well, not_ the _Xerneas anyway… but I am_ a _Xerneas, if that makes any sense…_

The girl frowned. "No, not really."

 _It's kind of a long story…_ Serena said, unsure if she should tell this girl.

"I'm not going anywhere," the girl said, pointing at her leg.

Serena paused. She couldn't really think of a reason to _not_ tell her story… besides, it was nice to have someone to talk to.

 _What's your name?_

"Kayla."

 _Well, Kayla,_ Serena began, settling down in the grass near the girl. _I guess it all started with the outbreak of the plague. It actually began with a completely normal day, but by the end of that week I was never the same again; none of us were..._


	2. Chapter 1 - Gathering Clouds

**Chapter 1: Gathering Clouds**

No one really knew for sure how or where it began.

All Serena knew was that she had been with her Pokemon when it first happened.

She was training with her Braixen, Pancham, and Sylveon outside the Pokemon Center when she overheard a group of trainers talking nearby.

"I don't know what happened," one girl was saying, practically in tears, "Lillipup was fine this morning. It ate all its food and it's been full of energy all day, but I noticed it was a little warm and glassy-eyed a few hours ago so I brought it to the Pokemon Center. Almost as soon as we got through the doors it was shaking terribly and whimpering. Nurse Joy has it now, but I'm scared; it just got sick so fast and out of nowhere too…"

"Did you say it was shaking? My Caterpie did that yesterday, but it seems fine today."

"Yeah, there's some kind of bug going around, but don't worry, your Lillipup will be fine, I'm sure!"

Serena listened on, a little concerned. She didn't want any of her Pokemon getting sick.

 _I'll tell the others later; we should probably leave tomorrow morning. I'd hate for any of them to get sick._

Satisfied, she turned back to her Pokemon and continued with training.

She would come to regret not leaving immediately; not that it would have mattered anyway.

...

"Wow, I'm starving!" Serena said as she entered the Center with her Pokemon, who all called out in agreement. She spotted Ash and the others with a blonde-haired girl at the counter getting back their Pokemon from Nurse Joy.

"Serena!" Bonnie cried, rushing over to her, "You missed it! Ash just battled the coolest Pokemon! You see that girl over there? Her name's Andrea and she has an Absol that can Mega Evolve! It was so cool! Come meet her; I tried setting her up with my brother, but you know how he is…"

Serena laughed as she was pulled along by a chattering Bonnie; weaving through a crowd that had come out of nowhere. When they found the others, Andrea was gone. She had apparently left for dinner with some friends.

"Aw!" Bonnie protested, pouting at her brother.

"Hey, don't shoot the messenger," he said, "Let's just go ahead and eat. I'm sure we'll see her again later; we can introduce her to Serena then, okay?"

"Did you at least ask her on a date-"

"NO, BONNIE!"

Serena left the arguing siblings and joined Ash (who had already gotten food and a table) and chatted with him about his battle and her performance training while they set up food bowls for their Pokemon. Clemont and Bonnie joined them, and they talked for hours about their Pokemon. After a little while, Serena mentioned the conversation she overheard earlier and the others agreed they should leave early in the morning. They weren't too worried, but no one wants their Pokemon to get sick.

They stayed up pretty late; only when Bonnie's head met the table with a snore did the older kids decide it was time to retire for the night.

...

Serena woke suddenly.

She wasn't sure what woke her at first, but a horrible scream soon gave her an idea.

She bolted out of bed and saw the others were awake as well. Ash had jumped out of his bed and hit the lights. All of them sat still, hearts pounding, waiting…

Another scream echoed from down the hall, ending in a sob; and Ash immediately threw the door open and raced down the hall, Pikachu at his heels. Serena and the others took one look at each other and followed.

They rounded a corner and saw a group of trainers who had also been woken by the noise standing in a semicircle in the lobby.

"I don't understand!" a voice wailed, "It was fine when I went to bed, it was just a little cough…"

They pushed their way through the crowd to where Ash was standing, at the front. A girl was sitting on the floor sobbing, clutching at very limp Vulpix. Serena froze in horror. Nurse Joy was trying to calm the girl down, but nothing was working.

"It was just a little cough," the girl sobbed, rocking back and forth "I don't understand…"

"Everyone, please, go back to your rooms!" Nurse Joy called as the girl's heartbroken wailing began again.

Serena put a hand on Bonnie's shoulder, steering her shaking form away as Nurse Joy's Wigglytuff ushered everyone out of the room.

Serena and the others went back to their room and sat on their beds with lights still on. Bonnie was pressed to her brother, still shaking while she held Dedenne close. Squishy sat by the window, visibly anxious as it stared up at the sky.

"Clemont…" Bonnie began quietly, "Was that Vulpix… dead?"

Clemont didn't say anything at first, but then: "Yes, Bonnie, it was."

Bonnie held Dedenne tighter and shrank closer to her brother. "What happened to it?"

"It was just a cough," Ash said, sounding stunned, "When I first got there, the girl was crying about how she had just taken Vulpix to Nurse Joy for a cough before she went to bed. Apparently, Nurse Joy had told her she was keeping Vulpix overnight, just for a good rest; but when she went in to check on it, it temperature was high and it couldn't breathe. It just… died. And she has no idea why."

"That's scary…" Serena whispered.

"Can we leave now?" Bonnie whimpered.

"The next town's pretty far Bonnie, and we need rest to make that trip," Clemont said, though his expression indicated he wanted to leave as well, "But I promise you, we'll leave first thing in the morning."

 _Like any of us will sleep after that._ Serena thought, laying down on her bed and trying to get the image of the Vulpix's wide, empty eyes out of her head.

...

They were packed and ready to go before the sun had even come up. They walked briskly toward the lobby, surrounded by other trainers just as determined to leave.

The atmosphere was somber, and all conversations were kept low and quiet. Serena didn't see the Vulpix's trainer anywhere…

What do you do in a situation like that? How would you deal with it? Serena didn't think she could stand it if it happened to her. She had to fight the urge to call Sylveon out of its Pokeball and grip onto it for dear life. Dedenne and Squishy were hidden away in Bonnie's bag, and Ash held Pikachu to his chest, almost tucked under his jacket. It was as if they believed they could hide their Pokemon from whatever killed that Vulpix last night…

Serena shook herself as they exited the building and continued on their journey. She needed to stop this; thoughts like that were just going to drive her crazy.

...

The sun was high in the sky. The crystal blue sky and gently breeze did not reflect the travelers' dim moods in the slightest.

Serena walked a little behind the others, yawning for the hundredth time. She hadn't slept much and it was starting to catch up to her. Braixen trotted alongside her, watching its trainer out of the corner of its eye. Serena caught its gaze and shook her head, stifling another yawn.

"I'm fine, Braixen. Don't worry about me."

The young fox Pokemon smiled at its trainer. Reassured, it skipped over to Bonnie to playfully tug at Dedenne's tail and chatter happily with the small Pokemon.

Serena smiled for a moment before returning to her own thoughts. She was worried about what happened to that Vulpix. She'd never seen anything like that before and she couldn't shake this feeling of dread growing inside her. What if was some kind of contagious disease? What if any of their Pokemon got it? She didn't know what she'd do…

She glanced back at Braixen, who was now carrying Dedenne against its fur while they chatted pleasantly alongside Bonnie. Serena forced herself to calm down. They seemed fine, and worrying wasn't going to help anyone.

That didn't get the image of that Vulpix's blank, dead eyes of her head though.

She sniffed a little, rubbing a hand across her eyes and trying to straighten herself up. She looked back up at her friends, just in time to see the blue of Clemont's eye before he faced forward again to pretend he didn't see anything.

Great. Now he was probably going to stop the group for a rest on her account.

Though, would that really be a bad thing? She was _really_ tired…

Sure enough, Clemont stretched and yawned.

"Hey, guys, I'm exhausted. Would anyone mind if we stopped for a little while? I could sure use a nap..."

Serena heard chimes of agreement from everyone else. Bonnie didn't even pick on her brother for wanting a break. Serena guessed everyone must be tired after last night.

The group veered of the path to look for a place to set up camp.

...

Luxray coughed for the third time that evening.

The large black Pokemon was lying behind Clemont while everyone sat around the fire to eat. Serena watched it nervously as its body was racked with deep-throated coughs. All light conversation had faded at this particular fit, which had gone on the longest. Luxray recovered, shaking its head a little before realizing everyone's gaze was on it. It shifted uncomfortably, muttering something under its breath before clearing its throat and turning away from the group to curl up behind its trainer and fall asleep.

Clemont reached around to pet Luxray with slow, rhythmic strokes until the Pokémon's breathing slowed as it drifted off to sleep.

Bonnie crawled over to Clemont and his Pokemon.

"Is Luxray okay?" she asked quietly, putting a tiny hand on one of Luxray's huge paws.

"Of course," Clemont said immediately, "It's probably just a cold or something."

Bonnie hesitated. "But that Vulpix just had a cough too! You don't think Luxray's sick, do you?"

Clemont thought for a moment. "It's possible that whatever was wrong with that Vulpix was an ongoing condition that wasn't caught in time," he reasoned, "It's uncommon, but Fire-type Pokemon have been known to suffer from respiratory problems that arise from developmental disorders… Basically, their lungs don't grow the way they're supposed to when they're in their eggs. Some Pokemon doctors believe it has something to do with the ability to breathe fire, and the anatomy that surrounds their lungs as a result."

He shrugged. "I doubt it was something infectious; I mean they usually put out warnings for contagious diseases, we would've heard something by now, right?"

Everyone relaxed a little. Serena felt Sylveon crawl onto her lap. She looked down at her sleeping Pokemon with a smile, gently rubbing its back.

Ash hadn't had much to say through all this. Serena supposed it was because of the Vulpix. With how deeply Ash cared for everything he came into contact with, it was no wonder the death of that Vulpix disturbed him. Serena noticed he hadn't eaten much, he had set his plate aside for Chespin to gleefully devour some time ago. Now he sat cross-legged on the grass with Pikachu asleep in his lap. She tried to think of something to say to him but was interrupted by a sudden sneeze from the Pokemon in her lap. Serena jumped a little, patting Sylveon as it sneezed twice more and made a strange whining sound.

Puzzled Serena gently shook Sylveon awake. The Pokemon whined again, pushing Serena's hand away with one of its ribbons and rolling over.

"Hey, are you alright?" Serena asked. Concerned, she lifted Sylveon up off her lap, intending to turn it around so she could see its face.

That is, until she saw the droplets of blood that had been sprayed across her skirt.

Serena stood up, screaming, causing everyone around her to jump to their feet as well.

"Sylveon!?" she sobbed, "Answer me!"

She cradled the little Pokemon in her arms, just now feeling how warm it was…

Oh, Arceus. Sylveon was sick, this is what she was afraid of! What was she going to do, she couldn't let it die. She was faintly aware of her friends asking frantic questions, but couldn't find a way to respond. It was like they were calling to her through a fog, and all she could see was Sylveon, limp and too warm, with blood running from its nose down its face...

Serena felt something cut through her panic; tiny paws pressed against her legs. She looked down to see Bunnelby and Chespin looking up at Sylveon, worry on their faces.

Serena tried to calm down and think.

"Here," Clemont said, "Let me see."

Bless him, he was already at her side with his bag of medical supplies. Serena reached over to hand Sylveon to him, but Sylveon let out another pitiful sneeze, spraying Clemont's sleeve with blood. Bonnie whimpered and Serena could literally see Clemont shoving his panic aside.

"There, there," he said, sounding surprisingly calm, "let's see what's wrong with you…"

He took a rag out of his pocket and gently wiped the blood off of Sylveon's face. He held a hand against its chest for a minute.

"I don't know why it's bleeding, and it's unresponsive, but at least its breathing and heart rate seem normal. I'll give it something for the fever. We should get it to a Pokemon Center soon though. There's not much I can do for it here."

"Okay." Serena said numbly, taking Sylveon back, and pressing into her chest. "Let's go now."

"Uh, Serena…"

"Don't, Clemont! We have to go now. It's _dying!_ "

"Serena, I understand, believe me, I do. But we can't go wandering around in the dark! It won't do Sylveon any good to be lost in the forest. I don't think any of us could even find the road in this darkness."

Serena couldn't argue with that. She sank to her knees, holding Sylveon close to her heart.

"What do I do, then?" she whispered.

"Make it comfortable. We didn't get far from that Pokemon Center, we can go back there at first light."

Luxray began coughing again. Clemont left to go sit by its side, looking concerned now. Bonnie joined them, curling up against her brother and crying quietly against the bag her little friends were nestled inside of.

Serena sat on her sleeping bag, wrapping Sylveon in an extra blanket and laying it on her pillow. There was no more blood on its face, and its fever already seemed to be going down, thanks to Clemont.

Serena realized Braixen and Pancham were by her side, watching over their teammate as well. But another presence caught her attention.

Ash had moved over to sit beside her. "Mind if Pikachu and I hang out with you? I don't think we're gonna get much sleep tonight. We wanna help keep an eye on Sylveon."

"Pi-ka!"

"Of course," Serena said quietly, "Thank you."

She shifted herself around until she was lying beside Sylveon, and she placed one on its side, to reassure herself that it was still breathing. She felt movement next to them, and craned her head over to see that Bunnelby and Chespin had curled up alongside Sylveon. Serena heard Sylveon muttering in its sleep, as it felt them curling up beside it.

Serena blinked back tears.

It was going to be a long night.

...

Serena woke to the sound of a heartbroken wail.

She jerked awake, immediately checking on Sylveon, but relaxed, a little confused, when she saw it was fine.

Sobbing drew her attention to the other side of the camp, where Clemont was laying over a very still Luxray. Bonnie stood by her brother, crying uncontrollably. Squishy was peering out of its bag, looking horrified.

Serena was on her feet in an instant, wrapping her arms around Bonnie and watching Clemont as tears filled her own eyes.

Clemont's fingers dug into Luxray's fur and his whole body shook with sobs. His other Pokemon stood by him, staring at Luxray in shock.

Ash knelt by Clemont, putting a hand on Luxray and saying something quietly in Clemont's ear.

"I don't know, I just found it like this when I left the tent," Clemont choked out between gasps, "I… I… don't…"

He pressed his head into Ash's shoulder and continued to sob. Bonnie tore out of Serena's grasp and fled back to the tent. Serena let her go, and moved to sit at Clemont's side. The other Pokemon had moved to stand around them, crying softly for Luxray.

She put a hand on Luxray's head. She could see blood leaking from it mouth and the corner of its eyes...

With a gasp, Serena leaped up.

"Sylveon!" she cried, running back to her sleeping Pokemon.

"Go!" Clemont called to her suddenly, raising head from Ash's shoulder and looking desperate, "Just take Sylveon and run to the Center! We'll catch up later."

Serena didn't waste any time. She scooped up her Pokemon and hit the road running.


End file.
